timesaveR

My daily work mostly entails running the same data cleaning, pre- and post-processing functions over and over again. For weeks, and weeks. Months. Years.

This rough R package includes a collections of functions doing the completely different things, their only common denominator is that they save me time.

Installation

devtools::install_github("alesssia/timesaveR")

Dependencies

R: https://www.r-project.org/
devtools: https://github.com/r-lib/devtools
Functions calculating linkage disequilibrium statistics query the LDproxy Programmatic Access via API. This requires a LDlink personal token, that can be requested here.

License

timesaveR is licensed under GNU GPL v3.

Acknowledgements

While some of the functions have been developed 100% by me, others are liberal (or not so liberal) adaptations of other people's work, several of whom I had lost track. I am happy to include attribution whenever I can: if you spot your or someone else's work, please let me know.

Changelog

0.0.1.6 / 2023-12-21

Enhancements:

Added a second function (LDtrait) that queries the GWAS Catalog this time via the LDproxy Programmatic Access
LDproxy returns also the queried SNP (rsID)
All functions based on the LDproxy Programmatic Access are now suppressing messages written to stderr.

0.0.1.5 / 2023-08-04

Enhancements:

Improved inverse.normal
Improved handling of errors/warning in LDproxy
estimate.heritability now checks the confidence intervals when extracting the best model

0.0.1.4 / 2020-09-02

Enhancements:

Improved handling of errors when linkage disequilibrium statistics are used
biomart.SNP.position can now return also the variant alleles
Added a function (biomart.SNP.rsID) that returns the rsID given the chromosomal coordinates and the alleles

0.0.1.3 / 2020-02-05

Enhancements:

Functions biomart.SNPid.in.window can now return also the variant alleles

0.0.1.2 / 2019-10-25

Enhancements:

Functions biomart.*.in.window can now return also the chromosomal coordinates
Added a function (biomart.SNP.position) that returns the chromosomal coordinates of a given SNP
Added functions to query the GWAS Catalog (GWAS.catalog.SNP and GWAS.catalog.SNP.proxy)